# Query on a recurring error during md simulation

**URL:** <https://gromacs.bioexcel.eu/t/query-on-a-recurring-error-during-md-simulation/9849>\
**Category:** User discussions\
**Created:** [August 9, 2024, 11:53am UTC](https://gromacs.bioexcel.eu/t/query-on-a-recurring-error-during-md-simulation/9849 "2024-08-09T11:53:52Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![debopom](https://avatars.discourse-cdn.com/v4/letter/d/85e7bf/32.png) [@debopom](https://gromacs.bioexcel.eu/u/debopom)\
**Post date:** [August 9, 2024, 11:53am UTC](https://gromacs.bioexcel.eu/t/query-on-a-recurring-error-during-md-simulation/9849/1 "2024-08-09T11:53:52Z")

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GROMACS version 2024.2:  
GROMACS modification: Yes/No  
Here post your question - During my working on md simulation using gromacs for my summer project, i am continuously getting stuck at the adding ion step of gromacs protein-ligand complex tutorial, the error is about the topology coordinates not matching the sol.gro coordinates, but i am following the steps to the utmost precision without any fault and even then this specific error is occuring.

 ![Screenshot 2024-08-09 171913](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/4/4e769327dd6b5059caccce117f592b91059cd85b.png)  
this following error is occuring, please help me in solving this error, your help will be much appreciated.

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**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [August 9, 2024, 1:25pm UTC](https://gromacs.bioexcel.eu/t/query-on-a-recurring-error-during-md-simulation/9849/2 "2024-08-09T13:25:51Z")

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My guess is you forgot to remove the water molecules from the topology file that you replaced by ions.

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<div class="post-metadata">

**Author:** ![debopom](https://avatars.discourse-cdn.com/v4/letter/d/85e7bf/32.png) [@debopom](https://gromacs.bioexcel.eu/u/debopom)\
**Post date:** [August 9, 2024, 1:35pm UTC](https://gromacs.bioexcel.eu/t/query-on-a-recurring-error-during-md-simulation/9849/3 "2024-08-09T13:35:46Z")

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But I haven’t had the chance to add ions, I had created the topology file of receptor-ligand complex using the gro file and then solvate the gro file.